A couple things you mentioned about your ladder test were dropping velocities and point of impact being lower with a higher charge or velocity...you said this was making you doubt your chrony.
First, I've shot over a chrony for years and only changed a few months ago. The problems I've experience coincide with other reviews, namely err readings and erratic velocities due to lighting or low battery...like 2754, 2767, 3290, 2756 That stuff sticks way out. The other problem with chrony is people who double check with superior equipment or methods report the "true" velocity can be 100fps different. In my experience, with a fresh battery and diffusers in place you will get consistent readings that give a good indication of your load's performance...ie exactly what you are after es&sd.
About velocity dropping while doing ladder tests...it happens often when I use book start loads between 10&15% below max until about 5-7% below max... from 5% below to max they tend to be the most linear until around max when recoil goes up but velocity levels or drops(not always true, but mostly from my experience).
About a lower impact at higher charge/chrony reading...this is not chrony error it's physics(first explained to me by my brother in law). Recoil begins at primer ignition as does the bullet's journey down the barrel. Most rifles have muzzle rise during recoil so a slower load allows the barrel to rise more before the bullet exits the muzzle. A higher velocity load allows the bullet to leave at an earlier(lower muzzle) point in the recoil cycle. I have noticed during a ladder test with charge increments of 0.5gr that a higher charge with a big increase in velocity results in a lower impact. So don't second guess your chrony because of a change in poi.
I have missed steps in reloading as well as made assumptions. Please post a detailed step by step, there might be something one of the guys can spot in your process that could make all the difference.
Do you weigh your brass? I'm not talking about sorting to groups of 0.1grs...I tried that(not really, more like sorted to 1gr). But I did find some that were way out like 5grs. If you have a piece per group it could open up the group.
The last point made me think, would you be able to post your velocities for a given string? It might be helpful to know if there's 1 in 5 that's way off or if they're just all over the map. Ie. Are you #s like 2670,2689, 2656, 2693, 2661......or are they 2705, 2701, 2711, 2640, 2709.
Lastly you mentioned switching primers as an option, that may be worth a try. More than a few people have had issues with Win primers lately. I dont know anything about moisin firing pins but you may get more consistent results with a harder primer like a CCI(I'm not a primer expert so someone please correct if this is wrong).
Good luck and keep trying, posting results, and asking questions...its more fun when we work together as a team. I would have given up and sold off a good rifle if it wasn't for the support of a reloading forum.
Willy